Umm.... Guys, I 've got an idea bout how 343 got all his info about the PoA and her systems. Alright, here I go. If the Cole Protocol was used there would have been nothing left right? I was reading the Fall of Reach again a couple days back and i go to the part where Capitain Keyes is on the Pillar of Autum for the first time. On page 273 Hikowa mentions that the Pillar of Autum has more that one AI.

"We've got more than that sir," Hikowa replied "Cortana is running the shakedown and supervising Dr. Halsey's modifacations to the ship. We have a second AI to handle point defense."

"Really?" Keyes was surprised; getting a single AI was tough enough these days. Getting two was unprecedented.

This shows that there were two AI's on the PoA before she went down!!!!! This also shows possibly where GS got the information about the ship. The Cole Protocol was probably carried out, but the Captain forgot about the second AI!!!! He said it himself! Getting one was hard, getting two is impossible. In all the excitement, he forgot...

Beowulf, or perhaps a lowly door operator? It is mentioned on page 290 of The Fall of Reach that with the Covenant blitzkrieg, there wasn't going to be time to boot up the second AI. As if that could stop a Bungie AI from making an appearance ;)

As we know, very few things are casually dropped around the Bungie camps. If you trip on it, it was probably put there for more than a laugh at your expense...